Liens

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 Charles Plessy, open-source biologist
 -------------------------------------
 
-My training as a researcher started with **developmental genetics in
-drosophila and zebrafish**, where I studied the activity of
-transcription enhancers ([Blader and coll.,
-2003](https://pubmed.gov/12559493)) and their evolutionary
-conservation (Plessy et al., 2005). This gave me a strong interest for
-whole-transcriptome analysis and technology. For that purpose, I have
-joined RIKEN in 2004, where have worked on high-throughput methods for
-**profiling promoters and inferring gene networks**, and in particular on
-CAGE (Cap Analysis Gene Expression).
+My training as a researcher started with **developmental genetics in drosophila
+and zebrafish**, where I studied the activity of transcription enhancers
+([Blader and coll., 2003](https://pubmed.gov/12559493)) and their evolutionary
+conservation ([Plessy and coll., 2005](https://pubmed.gov/15797614)). This gave
+me a strong interest for whole-transcriptome analysis and technology. For that
+purpose, I have joined RIKEN in 2004, where have worked on high-throughput
+methods for **profiling promoters and inferring gene networks**, and in
+particular on CAGE (Cap Analysis Gene Expression).
 
 I have developed a miniaturized version of CAGE, termed **nanoCAGE**, to
-analyse small samples yielding only nanograms of RNA (Plessy et al.,
-2010). In the same manuscript, we also introduced its paired-end
-variant, **CAGEscan**, which we use to **associate novel promoters with
-annotations**. Since then, we have kept improving or expanding these
-techniques, by updating the protocol (Salimullah et al., 2011),
-reducing the sequence bias introduced by the molecular barcodes (Tang
-et al., 2013), combining multiple cap-enrichment steps (Batut et al.,
-2013), benchmarking the use of locked nucleic acids for template
-switching (Harbers et al., 2013), and reducing the number of primer
+analyse small samples yielding only nanograms of RNA ([Plessy and coll.,
+2010](https://pubmed.gov/20543846)). In the same manuscript, we also introduced
+its paired-end variant, **CAGEscan**, which we use to **associate novel
+promoters with annotations**. Since then, we have kept improving or expanding
+these techniques, by updating the protocol ([Salimullah and coll.,
+2011](https://pubmed.gov/21205859)), reducing the sequence bias introduced by
+the molecular barcodes ([Tang and coll., 2013](https://pubmed.gov/23180801)),
+combining multiple cap-enrichment steps ([Batut and coll.,
+2013](https://pubmed.gov/22936248)), benchmarking the use of locked nucleic
+acids for template switching ([Harbers and coll.,
+2013](https://pubmed.gov/24079827)), and reducing the number of primer
 artefacts and unwanted sequences generated by ribosomal RNAs using
-low-complexity “pseudo-random” reverse-transcription primers (Arnaud
-et al., 2016).
+low-complexity “pseudo-random” reverse-transcription primers ([Arnaud and
+coll., 2016](https://pubmed.gov/27071605)).
 
 On April 2013, I started a new development cycle as the leader of the
 Genomics Miniaturization Technology Unit at RIKEN Center for Life